Currently, the ProbABEL output only lists the chi^2 value (calculated via the likelihood ratio test) in the last column of the output. We are planning to add p-value support to the output as well , and work is on the way , but since I don't have direct funding for ProbABEL development anymore, this ...

Thanks for joining the forum. I will try and see if I can reproduce this. I happen to have to convert some imputed data in VCF format to DatABEL files myself. I will get back to you in a couple of days.

I don't think anybody ever used GenABEL with that many subjects. Maybe it works, maybe it won't. Do I understand correctly that you don't have genetic data, only pedigree information? It has been a while since I used GenABEL for family data, but I seem to remember it only uses genetic data to determ...

Did you be any chance create the file on Windows and use it on Linux, or the other way around? This could be the result of the different ways Linux and Windows encode the "end-of-line" character. If you created the file on Windows and now run on Linux, please use the 'dos2unix' tool to con...

I think it would be possible with some modifications. Of course. With modifications it would work. However, given that this goes down to the level of the data model, it won't be "some" modifications. It will be quite some work because many (all?) functions in the GenABEL package would nee...

Glad to hear you kept looking into this issue (even without bioinformatics training). I appreciate it a lot if people show willingness to dive into a problem and look/try/experiment a bit further, instead of just saying: "it doesn't work, tell me what I should type to fix it". :D Update: I...

Thanks to Maarten ( see the Github issue ) I now know how I missed the memory leaks in the v0.5.0 release (the Jenkins build checks had silently failed after an upgrade). In the mean time I also fixed the issue. Do you have time to test the latest commit in the Git master branch? Or, if you haven't ...